Diffraction before destruction

X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.

[1]  H. Chapman,et al.  Determination of multiwavelength anomalous diffraction coefficients at high x-ray intensity , 2013, 1305.3489.

[2]  R. Henderson The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules , 1995, Quarterly Reviews of Biophysics.

[3]  Elspeth F Garman,et al.  Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE. , 2009, Journal of synchrotron radiation.

[4]  R. London,et al.  Encapsulation and diffraction-pattern-correction methods to reduce the effect of damage in x-ray diffraction imaging of single biological molecules. , 2007, Physical review letters.

[5]  J. Frank Three-Dimensional Electron Microscopy of Macromolecular Assemblies , 2006 .

[6]  E. Girard,et al.  Reduction of radiation damage and other benefits of short wavelengths for macromolecular crystallography data collection , 2012 .

[7]  Sébastien Boutet,et al.  Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature , 2013, Science.

[8]  Carl Caleman,et al.  Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses , 2011 .

[9]  Anton Barty,et al.  Room-temperature macromolecular serial crystallography using synchrotron radiation , 2014, IUCrJ.

[10]  Georg Weidenspointner,et al.  Lipidic phase membrane protein serial femtosecond crystallography , 2012, Nature Methods.

[11]  B. Ziaja,et al.  Modelling dynamics of samples exposed to free-electron-laser radiation with Boltzmann equations , 2006 .

[12]  Auger-electron cascades in diamond and amorphous carbon , 2001, cond-mat/0109430.

[13]  S. Marchesini,et al.  SPEDEN: reconstructing single particles from their diffraction patterns. , 2004, Acta crystallographica. Section A, Foundations of crystallography.

[14]  G. Taylor The phase problem. , 2003, Acta crystallographica. Section D, Biological crystallography.

[15]  Sean McSweeney,et al.  Specific radiation damage can be used to solve macromolecular crystal structures. , 2003, Structure.

[16]  Georg Weidenspointner,et al.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. , 2011, Physical review. B, Condensed matter and materials physics.

[17]  L. Cercek,et al.  Pulse-radiolysis study of a biological matrix. , 1973, International journal of radiation biology and related studies in physics, chemistry, and medicine.

[18]  Elspeth F Garman,et al.  Experimental determination of the radiation dose limit for cryocooled protein crystals. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. T. Pratt,et al.  Femtosecond electronic response of atoms to ultra-intense X-rays , 2010, Nature.

[20]  J. Chalupský,et al.  Creation and diagnosis of a solid-density plasma with an X-ray free-electron laser , 2012, Nature.

[21]  Anton Barty,et al.  Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data , 2014, Journal of applied crystallography.

[22]  Kenneth A. Frankel,et al.  The minimum crystal size needed for a complete diffraction data set , 2010, Acta crystallographica. Section D, Biological crystallography.

[23]  Anton Barty,et al.  Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography , 2013, Nature Communications.

[24]  D Rolles,et al.  Ultraintense x-ray induced ionization, dissociation, and frustrated absorption in molecular nitrogen. , 2010, Physical review letters.

[25]  J. Kirz,et al.  An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. , 2005, Journal of Electron Spectroscopy and Related Phenomena.

[26]  James M. Holton,et al.  A beginner’s guide to radiation damage , 2009, Journal of synchrotron radiation.

[27]  Carl Caleman,et al.  Auger electron cascades in water and ice , 2004 .

[28]  C. Bostedt,et al.  Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. , 2013, Physical review letters.

[29]  Janos Hajdu,et al.  Radiation-induced electron cascade in diamond and amorphous carbon , 2001, SPIE Optics + Photonics.

[30]  E. Garman,et al.  Radiation damage to biological macromolecules: some answers and more questions. , 2013, Journal of synchrotron radiation.

[31]  Sang-Kil Son,et al.  Multiwavelength anomalous diffraction at high x-ray intensity. , 2011, Physical review letters.

[32]  Sébastien Boutet,et al.  The Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) , 2010 .

[33]  Anton Barty,et al.  CrystFEL: a software suite for snapshot serial crystallography , 2012 .

[34]  K. Schmidt,et al.  Gas dynamic virtual nozzle for generation of microscopic droplet streams , 2008, 0803.4181.

[35]  J. Hajdu,et al.  Potential for biomolecular imaging with femtosecond X-ray pulses , 2000, Nature.

[36]  M. Klintenberg,et al.  Radiation damage in biological material: Electronic properties and electron impact ionization in urea , 2008, 0808.1197.

[37]  S. Schreck,et al.  Stimulated X-ray emission for materials science , 2013, Nature.

[38]  A. Authier,et al.  Diffraction Physics , 1998 .

[39]  Georg Weidenspointner,et al.  Femtosecond X-ray protein nanocrystallography , 2011, Nature.

[40]  Georg Weidenspointner,et al.  Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements , 2011, Nature Photonics.

[41]  H. Chapman,et al.  Femtosecond protein nanocrystallography-data analysis methods. , 2010, Optics express.

[42]  Garth J. Williams,et al.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography , 2012, Science.

[43]  Sang-Kil Son,et al.  Impact of hollow-atom formation on coherent x-ray scattering at high intensity , 2011, 1101.4932.

[44]  Abraham Szoke,et al.  Dynamics of biological molecules irradiated by short x-ray pulses. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[45]  J. Campbell,et al.  WIDTHS OF THE ATOMIC K–N7 LEVELS , 2001 .

[46]  Anton Barty,et al.  Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser , 2013, Science.

[47]  B. L. Henke,et al.  X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92 , 1993 .

[48]  H. Chapman,et al.  On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. , 2011, ACS nano.

[49]  Henry N. Chapman,et al.  Serial crystallography on in vivo grown microcrystals using synchrotron radiation , 2014, IUCrJ.

[50]  Sébastien Boutet,et al.  De novo protein crystal structure determination from X-ray free-electron laser data , 2013, Nature.

[51]  J. Hajdu,et al.  Diffraction imaging of single particles and biomolecules. , 2003, Journal of structural biology.

[52]  Hugh T. Philipp,et al.  Pixel array detector for X-ray free electron laser experiments , 2011 .

[53]  D. Ratner,et al.  First lasing and operation of an ångstrom-wavelength free-electron laser , 2010 .

[54]  J. Solem,et al.  Microholography of Living Organisms , 1982, Science.

[55]  Anton Barty,et al.  Crystallographic data processing for free-electron laser sources , 2013, Acta crystallographica. Section D, Biological crystallography.

[56]  Richard A. London,et al.  Unified model of secondary electron cascades in diamond , 2004 .

[57]  Gianluca Geloni,et al.  A novel self-seeding scheme for hard X-ray FELs , 2011 .

[58]  E. Garman,et al.  To scavenge or not to scavenge, that is STILL the question , 2012, Journal of synchrotron radiation.

[59]  R. Henning,et al.  Kinetic modeling of the X-ray-induced damage to a metalloprotein. , 2013, The journal of physical chemistry. B.